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DaehwanKimLab
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hisat2
Graph-based alignment (Hierarchical Graph FM index)
GNU General Public License v3.0
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forks not cleaned up when `-x` passed file that does not exist
#384
wholtz
opened
1 year ago
0
Hisat2 does not align almost exact reads with snptran index
#383
bgorissen
opened
1 year ago
0
(ERR): ValueError: invalid literal for int() with base 10: '.'
#382
poecile-palustris
opened
1 year ago
1
hisat-3n directional-mapping and repeat mode on single-cell methylome data
#381
lhqing
opened
1 year ago
2
error 134
#380
najibveto
opened
2 years ago
0
Ensembl uses a one-based coordinate system, whereas UCSC uses a zero-based coordinate system.
#379
CTLife
opened
2 years ago
0
hisat-3n for RNA align
#378
xieyy46
opened
2 years ago
5
long processing time solved by --no-temp-splicesite
#377
nickarouse
opened
2 years ago
0
BUG: exons and splice sites don't raise an error when supplied as the index
#376
t-f-freeman
opened
2 years ago
0
How to determine correct RNA strandness for single end reads?
#375
PVlasov93
opened
2 years ago
0
hisat-3n conda installation
#374
isaacvock
opened
2 years ago
3
(ERR): hisat2-align died with signal 7 (BUS)
#373
sylphjh
opened
2 years ago
1
Is it okay to increase number of missing genotypes to be filled?
#372
yunfeiguo
opened
2 years ago
0
Uniquely mapped reads
#371
JunxiFeng
opened
2 years ago
0
hisat2-build were killed when attempting to index the Ginkgo genome
#370
zoukai3412085
opened
2 years ago
9
Installing hisat2 with some problems
#369
Huang-XN
opened
2 years ago
0
Feature Request - Output hisat-3n-table count as a "bed format" or "bed-like" format
#368
aleighbrown
opened
2 years ago
0
The considerable increase of overall alignment rate after setting --very-sensitive
#367
SarahIsme
opened
2 years ago
2
fix hisat-3n unmapped deadname problem and improve alignment accuracy
#366
imzhangyun
closed
2 years ago
0
Integer overflow(?) in TLENs when insert should be reasonable
#365
IanSudbery
closed
2 years ago
2
update hisat-3n webpage for directional mapping mode
#364
imzhangyun
closed
2 years ago
0
add directional mapping mode for hisat-3n
#363
imzhangyun
closed
2 years ago
0
add --directional-mapping mode for hisat-3n
#362
imzhangyun
closed
2 years ago
0
compiling issue for HISAT-3N
#361
wbvguo
closed
2 years ago
2
hisat2 is not robust in term of short reads mapping
#360
y9c
closed
2 years ago
2
It's possible that insertions of up to 100 bps ?
#359
Wenfei-Xian
opened
2 years ago
1
Extract reads aligned concordantly exactly 1 time from hisat2 output (.sam file)
#358
poecile-palustris
opened
2 years ago
0
[Feature request] Directional mapping mode for hisat2-3n aligner
#357
y9c
closed
2 years ago
8
better way to classify YZ tag
#356
imzhangyun
closed
2 years ago
0
"Warning: a local graph exploded" when building hisat2 index
#355
eggrandio
opened
2 years ago
3
hisat-3n-table chrom name fixing
#354
imzhangyun
closed
2 years ago
0
fix the scoring problem. will filter out the alignment with low score
#353
imzhangyun
closed
2 years ago
0
(ERR): hisat2-align exited with value 137 on 128G RAM workstation
#352
ashish-apv
opened
2 years ago
2
`--score-min` do not work correctly for hisat2-3n
#351
y9c
closed
2 years ago
7
make temp dir more robust
#350
y9c
opened
2 years ago
1
make temp dir more robust
#349
y9c
opened
2 years ago
0
Memory Requirements to run alignment
#348
YasirKusay
closed
2 years ago
0
Hisat3n | Long mapping times
#347
ezecalvo
opened
2 years ago
0
Does hisat-3n-table count base by YZ tag or strandness for strand-specific RNA-seq data
#346
ifantasy
closed
2 years ago
1
New release of HISAT2
#345
asilvestris84
opened
2 years ago
0
(ERR): hisat2-align exited with value 139
#344
shrhops
opened
2 years ago
0
hisat2-build error: Could not allocate space for a joined string
#343
showteeth
opened
2 years ago
1
HISAT3N question about NM and MD tags
#342
aleighbrown
closed
2 years ago
2
SyntaxError
#341
hidvegin
closed
2 years ago
2
hisat2 is not compiling on M1 Mac
#340
rayhendricks
closed
1 year ago
3
fix typo
#339
imzhangyun
closed
2 years ago
0
Primary alignments of multi-mapping reads
#338
Li-Tianran
opened
2 years ago
0
Allow reporting one of the sam tags in `hisat-3n-table`
#337
vivekbhr
closed
2 years ago
4
Edit hisat-3n webpage for new feature: Zf tag and hisat-3n-table stdout
#336
imzhangyun
closed
2 years ago
0
add Zf tag for HISAT-3N. std out option for hisat-3n-table.
#335
imzhangyun
closed
2 years ago
0
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